Dynamic 3D chromatin remodeling in acute leukemia - Resubmission - 1

急性白血病的动态 3D 染色质重塑 - 重新提交 - 1

基本信息

批准号：
10364736
负责人：
Aristotelis Tsirigos
金额：
$ 60.52万
依托单位：
NEW YORK UNIVERSITY SCHOOL OF MEDICINE
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-04-01 至 2026-03-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10364736
关键词：
3-Dimensional Acute Lymphocytic Leukemia Acute T Cell Leukemia Acute leukemia Address Affect Architecture Automobile Driving Binding CRISPR interference CRISPR-mediated transcriptional activation CRISPR/Cas technology Cancer Patient Cell Maintenance Child Chromatin Chromatin Loop Clustered Regularly Interspaced Short Palindromic Repeats Computing Methodologies DNA Diagnosis Disease Disease remission Dissection Downstream Enhancer Drug resistance Enhancers Epigenetic Process Event Evolution Gene Expression Gene Expression Regulation Genes Genetic Genetic Enhancer Element Glioblastoma Growth Hi-C Human Hypermethylation IGF1R gene In Vitro Large-Scale Sequencing Light MYC gene Malignant Neoplasms Maps Mediating Methods NOTCH1 gene Neighborhoods Oncogene Activation Oncogenes Oncogenic Outcome Pathway interactions Patients Pharmaceutical Preparations Pharmacotherapy Point Mutation Prognosis Property Recurrence Regulation Regulator Genes Regulatory Element Relapse Resistance Role Sampling Structure T-Cell Development Techniques Technology Testing Thymus Gland Time Transcriptional Regulation Treatment outcome Tumor Suppressor Proteins Untranslated RNA Validation base cancer initiation chromatin remodeling chromosome conformation capture cohort differential expression drug relapse genome-wide in vivo insight leukemia metaplastic cell transformation new therapeutic target novel novel marker novel strategies pediatric acute leukemia promoter relapse patients targeted treatment therapy resistant tool transcription factor treatment response

项目摘要

ABSTRACT Recent advances in chromatin conformation capture techniques have revolutionized our understanding of chro- matin organization and have provided novel insights at an unprecedented level of detail. Several studies have identified biologically-relevant structures in DNA-DNA contact maps, such as A/B compartments, topologically- associating domains (TADs), insulated neighborhoods, and have elucidated the role of chromatin architecture in gene regulation and maintenance of cell identity. A handful of very recent studies from our lab and others have shown that aberrant TAD activation or “rewiring” promoter-enhancer interactions can promote cancer growth. However, no study has yet addressed the disruptions of chromatin organization on a genome-wide scale in cancer patients or how such disruptions modify the promoter-enhancer landscape leading to drug resistance and relapse. Using primary acute leukemia patient samples, we have, for the first time, identified recurrent TAD disruptions in leukemia involving key oncogenes (e.g. NOTCH1, MYC) and their targets. For example, we iden- tified a recurrent disruption of 3D chromatin topology in the MYC locus at a previously uncharacterized non- coding CTCF-bound region that insulates MYC from downstream enhancers. This disruption enables chromatin interactions between the MYC oncogene and the downstream enhancers leading to an increase in MYC expres- sion. Based on our preliminary results, we propose to investigate 3D chromosomal landscape reorganization as a new mechanism of cancer initiation, progression and relapse, and to discover novel non-coding regulatory elements (enhancer 3D hubs and their TAD boundaries) that drive leukemia. To this end, we will first profile and analyze a large cohort of leukemia patients using Hi-C and H3K27ac HiChIP both at diagnosis and at relapse to identify recurrent relapse-specific 3D reorganization events. We will combine computational methods with or- thogonal CRISPR strategies to discover transcription factors and epigenetic modifiers that enable the emergence of drug resistance via the rewiring of enhancer-promoter chromatin looping. We will then focus on enhancer hubs: we and others have shown that enhancers that are densely connected with target promoters and other enhancers (i.e. enhancer hubs) are robust regulators of gene expression and their disruption can impact the regulation of multiple genes. Based on these findings, we will test whether such enhancer hubs and their 3D topology can be drivers of drug resistance by activating oncogenic loci in vitro and in vivo. Our proposed study will not only elucidate the role of 3D architecture in leukemia at diagnosis and relapse, but it will also advance our understanding of resistance to therapy and develop new approaches to overcome it.

抽象的染色质构象捕获技术的最新进展已彻底改变了我们对CHRO的理解 Mattin组织，并以前所未有的细节提供了新颖的见解。有几项研究在DNA-DNA接触图中鉴定出与生物学相关的结构，例如A/B室，拓扑 - 关联域（TADS），绝缘邻居，并阐明了染色质结构在细胞身份的基因调节和维持。我们实验室和其他的少数最近的研究表明异常的TAD激活或“重新布线”启动子增强剂相互作用可以促进癌症的生长。但是，尚无研究以全基因组量表的染色质组织的中断癌症患者或这种干扰如何改变启动子增强剂景观，导致耐药性和复发。使用原发性急性白血病患者样品，我们首次确定了tad 涉及关键癌基因（例如Notch1，Myc）及其靶标的白血病的破坏。例如，我们识别在MYC基因座中，以先前未表征的非特征来调述了3D染色质拓扑的复发性破坏编码CTCF结合的区域，使MYC与下游增强剂绝缘。这种破坏使染色质启用 MYC癌基因与下游增强剂之间的相互作用导致MYC表达增加 - 锡。根据我们的初步结果，我们建议研究3D染色体景观重组癌症开始，进展和缓解的新机制，并发现新型的非编码调节元素（增强子3D枢纽及其TAD边界）驱动白血病。为此，我们将首先个人资料和使用HI-C和H3K27AC HICHIP分析大量的白血病患者，并在诊断方面进行救济确定反复继电器特定的3D重组事件。我们将将计算方法与OR-相结合 Thogonal CRISPR策略发现转录因素和表观遗传修饰符，使出现通过重新布线增强子促销染色质循环的耐药性。然后，我们将专注于增强器集线器：我们和其他人都表明，与目标启动子和其他人相关的增强子增强子（即增强子枢纽）是基因表达的强大调节剂，其破坏会影响调节多个基因。根据这些发现，我们将测试此类增强器中心及其3D是否拓扑可以通过在体外和体内激活致癌性局部来是耐药性的驱动因素。我们提出的研究不仅会阐明3D体系结构在白血病中的作用我们对耐药性的理解并开发了克服新方法。